Untitled Draft
Report Author
07 décembre, 2021
mask_siteid_sampling <- site_protocol_quanti[
site_protocol_quanti$variable == "year" &
site_protocol_quanti$n >= 10,
]$siteid
mask_siteid_protocol <- site_protocol_quali[
site_protocol_quali$unitabundance %in% c("Count", "Ind.100m2"), ]$siteid
mask_siteid <- mask_siteid_sampling[mask_siteid_sampling %in% mask_siteid_protocol]trends_data <- abun_rich_op %>%
left_join(op_protocol, by = "op_id") %>%
filter(siteid %in% mask_siteid) %>%
mutate(
log_total_abundance = log(total_abundance),
log_species_nb = log(species_nb)
)plot_community_data <- function(dataset = NULL, y = NULL, x = NULL, title = NULL) {
p <- dataset %>%
ggplot(aes_string(y = y, x = x)) +
geom_point() +
geom_smooth(method = "loess", formula = "y ~ x")
if (!is.null(title)) {
p <- p +
labs(title = title)
}
return(p)
}
plot_trends <- trends_data %>%
group_by(siteid) %>%
nest() %>%
ungroup() %>%
slice_sample(n = 100) %>%
mutate(
p_abun = map2(data, siteid,
~plot_community_data(
dataset = .x, y = "total_abundance", x = "year", title = .y)),
p_rich = map2(data, siteid,
~plot_community_data(
dataset = .x, y = "species_nb", x = "year", title = .y),
)
)0.1 Total abundance
n_plot_by_batch <- 8
map(
split(
seq_len(nrow(plot_trends)),
1:floor(nrow(plot_trends) / n_plot_by_batch) + 1),
~plot_grid(plotlist = plot_trends[.x, ]$p_abun)
)
#> Warning in split.default(seq_len(nrow(plot_trends)), 1:floor(nrow(plot_trends)/
#> n_plot_by_batch) + : la taille de données n'est pas un multiple de la variable
#> découpée
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 2007
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 2
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 0
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : pseudoinverse used at
#> 2007
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : neighborhood radius 2
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : reciprocal condition
#> number 0
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0.2 Species richness
map(
split(
seq_len(nrow(plot_trends)),
1:floor(nrow(plot_trends) / n_plot_by_batch) + 1
),
~plot_grid(plotlist = plot_trends[.x, ]$p_rich)
)
#> Warning in split.default(seq_len(nrow(plot_trends)), 1:floor(nrow(plot_trends)/
#> n_plot_by_batch) + : la taille de données n'est pas un multiple de la variable
#> découpée
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : pseudoinverse used at 2007
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : neighborhood radius 2
#> Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
#> parametric, : reciprocal condition number 0
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : pseudoinverse used at
#> 2007
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : neighborhood radius 2
#> Warning in predLoess(object$y, object$x, newx = if
#> (is.null(newdata)) object$x else if (is.data.frame(newdata))
#> as.matrix(model.frame(delete.response(terms(object)), : reciprocal condition
#> number 0
#> $`2`
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#> $`13`
0.3 Analysis
0.4 Reproducibility
Reproducibility receipt
## datetime
Sys.time()
#> [1] "2021-12-07 10:36:23 CST"
## repository
if(requireNamespace('git2r', quietly = TRUE)) {
git2r::repository()
} else {
c(
system2("git", args = c("log", "--name-status", "-1"), stdout = TRUE),
system2("git", args = c("remote", "-v"), stdout = TRUE)
)
}
#> Local: main /home/alain/Documents/post-these/isu/RivFishTimeBiodiversityFacets
#> Head: [45bbace] 2021-12-04: Add Rigal temporal analysis + finish the targets pipe
## session info
sessionInfo()
#> R version 4.0.5 (2021-03-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Debian GNU/Linux 10 (buster)
#>
#> Matrix products: default
#> BLAS: /home/alain/.Renv/versions/4.0.5/lib/R/lib/libRblas.so
#> LAPACK: /home/alain/.Renv/versions/4.0.5/lib/R/lib/libRlapack.so
#>
#> locale:
#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
#> [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] cowplot_1.1.1 rnaturalearthdata_0.1.0 rnaturalearth_0.1.0
#> [4] mapview_2.10.0 sf_0.9-7 rmarkdown_2.11
#> [7] scales_1.1.1 kableExtra_1.3.1 here_1.0.1
#> [10] magrittr_2.0.1 forcats_0.5.1 stringr_1.4.0
#> [13] dplyr_1.0.4 purrr_0.3.4 readr_2.1.1
#> [16] tidyr_1.1.2 tibble_3.1.6 ggplot2_3.3.3
#> [19] tidyverse_1.3.0 tarchetypes_0.3.2 targets_0.8.1
#> [22] conflicted_1.1.0 nvimcom_0.9-122
#>
#> loaded via a namespace (and not attached):
#> [1] leafem_0.1.6 colorspace_2.0-0 ellipsis_0.3.2 class_7.3-18
#> [5] leaflet_2.0.4.1 rprojroot_2.0.2 satellite_1.0.4 base64enc_0.1-3
#> [9] fs_1.5.1 rstudioapi_0.13 farver_2.0.3 fansi_0.5.0
#> [13] lubridate_1.7.9.2 xml2_1.3.2 codetools_0.2-18 splines_4.0.5
#> [17] cachem_1.0.4 knitr_1.36 jsonlite_1.7.2 broom_0.7.4
#> [21] dbplyr_2.1.0 png_0.1-7 compiler_4.0.5 httr_1.4.2
#> [25] backports_1.2.1 assertthat_0.2.1 Matrix_1.3-2 fastmap_1.1.0
#> [29] cli_3.1.0 htmltools_0.5.1.1 tools_4.0.5 igraph_1.2.6
#> [33] gtable_0.3.0 glue_1.5.1 Rcpp_1.0.6 cellranger_1.1.0
#> [37] jquerylib_0.1.3 raster_3.4-5 vctrs_0.3.8 nlme_3.1-152
#> [41] crosstalk_1.1.1 xfun_0.28 ps_1.6.0 rvest_0.3.6
#> [45] lifecycle_1.0.1 hms_1.1.1 yaml_2.2.1 memoise_2.0.0
#> [49] sass_0.3.1 stringi_1.7.6 highr_0.9 e1071_1.7-4
#> [53] rlang_0.4.12 pkgconfig_2.0.3 evaluate_0.14 lattice_0.20-41
#> [57] htmlwidgets_1.5.3 labeling_0.4.2 processx_3.5.2 tidyselect_1.1.1
#> [61] bookdown_0.24 R6_2.5.1 generics_0.1.0 DBI_1.1.1
#> [65] pillar_1.6.4 haven_2.3.1 withr_2.4.3 mgcv_1.8-34
#> [69] units_0.6-7 sp_1.4-5 modelr_0.1.8 crayon_1.4.2
#> [73] KernSmooth_2.23-18 utf8_1.2.2 tzdb_0.2.0 grid_4.0.5
#> [77] readxl_1.3.1 data.table_1.13.6 callr_3.7.0 git2r_0.29.0
#> [81] reprex_1.0.0 digest_0.6.27 classInt_0.4-3 webshot_0.5.2
#> [85] stats4_4.0.5 munsell_0.5.0 viridisLite_0.3.0 bslib_0.2.4